4J3X: Crystal structure of barley limit dextrinase (E510A mutant) in complex with a branched maltoheptasaccharide

Complete hydrolytic degradation of starch requires hydrolysis of both the alpha-1,4- and alpha-1,6-glucosidic bonds in amylopectin. Limit dextrinase (LD) is the only endogenous barley enzyme capable of hydrolyzing the alpha-1,6-glucosidic bond during seed germination, and impaired LD activity inevitably reduces the maltose and glucose yields from starch degradation. Crystal structures of barley LD and active-site mutants with natural substrates, products and substrate analogues were sought to better understand the facets of LD-substrate interactions that confine high activity of LD to branched maltooligosaccharides. For the first time, an intact alpha-1,6-glucosidically linked substrate spanning the active site of a LD or pullulanase has been trapped and characterized by crystallography. The crystal structure reveals both the branch and main-chain binding sites and is used to suggest a mechanism for nucleophilicity enhancement in the active site. The substrate, product and analogue complexes were further used to outline substrate binding subsites and substrate binding restraints and to suggest a mechanism for avoidance of dual alpha-1,6- and alpha-1,4-hydrolytic activity likely to be a biological necessity during starch synthesis.
PDB ID: 4J3XDownload
MMDB ID: 117433
PDB Deposition Date: 2013/2/6
Updated in MMDB: 2015/11
Experimental Method:
x-ray diffraction
Resolution: 1.75  Å
Source Organism:
Similar Structures:
Biological Unit for 4J3X: monomeric; determined by author and by software (PISA)
Molecular Components in 4J3X
Label Count Molecule
Protein (1 molecule)
Limit Dextrinase
Molecule annotation
Chemicals (18 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB